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Crystal structure of grl-8234 bound to bace (beta-secretase)

Analyse Crystal structure of grl-8234 bound to bace (beta-secretase) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VKM
Type: protein
Length: 1,556 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-secretase 1
UniProt: P56817
Ligands: BSD
Pockets: 10 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Beta-secretase 1	protein	389	15% helix, 38% strand	P56817

Ligands and binding sites

BSD · N-{(1S,2R)-1-benzyl-2-hydroxy-3-[(3-methoxybenzyl) amino]propyl}-5-[methyl(methylsulfonyl)amino]-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide · ligand · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	444	0.72	0.83	36	empty
2	524	0.72	0.81	72	BSD
3	501	0.71	0.81	63	BSD
4	413	0.71	0.82	31	empty
5	418	0.70	0.82	64	BSD

Interfaces

3 interfaces between chains.

A–D · 823 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 822 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 194 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2VKM · Crystal structure of GRL-8234 bound to BACE (Beta-secretase) · the same entry in another collection · chain D against D, TM-score 1.00
P56817 · AlphaFold monomer V2.0 prediction for beta-secretase 1 (P56817) · a predicted model of the same protein · chain C against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P56817
Elsewhere: RCSB PDB 2VKM · PDBe 2VKM · UniProt P56817

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